Israeli forces disguised in Palestinian clothes – including one impersonating a pregnant woman in a wheelchair – have raided a hospital in the flashpoint city of Hebron, shooting dead a relative of a man suspected of carrying out a stabbing attack.

The operation, involving two dozen undercover soldiers and Shin Bet agents – some wearing fake beards – took place in the early hours of Thursday morning.

During the raid, patients on the third floor of the al-Ahly hospital were confined to their wards. Hospitals are customarily regarded in conflicts as protected locations, even for enemy combatants.

The armed swoop – the second by Israeli forces on a Palestinian hospital this year – saw 27-year-old Abdallah Shalaldeh killed as he emerged from a bathroom in the ward where his cousin, Azzam, a Hamas member, was being treated for gunshot wounds.

The Israeli army confirmed the raid and shooting. It said Azzam Shalaldeh was suspected of stabbing an Israeli settler two weeks ago in the West Bank.

Hospital staff and eyewitnesses – including another relative of the two men – said troops had entered the hospital with guns hidden beneath the person pretending to be pregnant.

Jihad Shawar, the hospital’s director, said: “The undercover forces arrived at about 2.50 in the morning. There were 20-30 of them. They came to the main door pretending to be relatives of a woman going into labour and wanted to take her to surgery.

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“When they got into the reception area the woman stood up and they produced guns, including some hidden underneath her on the wheel chair. They went straight to the room on the third floor where Azzam Shalaldeh, who had been treated here since 25 October, was staying.

“They handcuffed his brother [Bilal Shalaldeh] with a belt. But when his cousin Abdallah came out of a bathroom on the ward they shot him five times before taking Azzam in the wheelchair they had brought. This is an outright crime. No one should violate hospitals.”

According to the Israeli authorities, Azzam Shalaldeh was being treated at the hospital for gunshot wounds, which the military said were sustained when the Israeli he allegedly stabbed last month shot him.

It said he was about 20 and from a family of “known Hamas operatives”.

Israel said Abdallah Shalaldeh was shot dead after grappling with soldiers – a claim denied by some Palestinian witnesses, who said he was shot as he left the bathroom. Others quoted anonymously in the Israeli media said there had been a scuffle.

Video footage of the incident shows about a dozen men walking down a hospital corridor, pushing someone covered in a blanket in a wheelchair. The person in the wheelchair flings the blanket off, stands up and, with the others, draws a gun and continues walking.

On the ward where Abdallah Shalaldeh was shot, a large pool of blood was visible on Thursday.

Mohammad Mayata was in a neighbouring room when he heard the shots. “I looked out the door and saw two people, one had a pistol and the other an M16,” he said. “When he saw me he said get inside or I’ll shoot you. When they had gone I came out and found a man lying in a pool of blood.”

Nidal Abdul Mutalib, 48, was also on the third floor when the soldiers entered. “I heard terrifying shots and panicked. I went outside. There was a man with a white beard and prayer cap shouting ‘Army! Army! Go back inside!’. The whole thing took eight to 10 minutes. I peeked out again and saw them taking away an injured man in a wheelchair with something covering his head.”

The footage also show the Israeli forces pushing a man in a wheelchair, apparently the suspect, back down the hall, as perplexed nurses look on.

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Speaking at Abdallah Shalaldeh’s funeral in the village of Sair outside Hebron later in the day, his cousin Blilal Shalaldeh described the raid. “It was around 3am and I was asleep when a large number of undercover soldiers arrived. They put the other patients in the corner and tied my hands with a belt. When Abdallah came out of the bathroom where he was washing his hands in preparation for morning prayers they shot him and left him to bleed on the floor.”

Last month, a group of men posing as Palestinian protesters and mingling with rock throwers in the West Bank were filmed suddenly drawing their weapons and arresting a protester.

The raid came amid ongoing violence that has lasted nearly two months. Twelve Israelis have been killed in a spate of attacks by Palestinians, while 78 Palestinians – 50 of them said by Israel to be attackers – have been killed.

The recent violence first erupted in Jerusalem over tensions surrounding a holy site sacred to both Jews and Muslims and quickly spread throughout Israel, the West Bank and the Gaza Strip.

Hebron, the largest West Bank city, has been a particular flashpoint. Several hundred Jewish settlers live in fortified enclaves in the city, amid tens of thousands of Palestinians.

In a statement defending, Shin Bet said it would “not permit terror operatives to hide in any places of refuge”.

Physicians for Human Rights-Israel, a non-profit rights group, accused Israeli forces of repeatedly violating the special protection afforded to hospital and medical facilities. “By doing so they are putting patients, hospital staff and visitors at risk,” it added.